[BioC] Error while building ExpressionSet from scratch....

[Bas Jansen]

Dear Martin, others,

Thanks for your help! It appears to be the data.frame <-> matrix problem.

Kind regards,
Bas

On Mon, Nov 14, 2011 at 6:35 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
> On 11/14/2011 04:37 AM, Bas Jansen wrote:
>>
>> Hi Bioconductor gurus:
>>
>> I am trying to make ExpressionSet files for the analysis of PCR
>> arrays, to be able to analyze them in LMGene. However, I get the
>> following error message:
>>
>>> eSet_xxx<- new("ExpressionSet", exprs = exprs_xxx, phenoData =
>>> phenoData_xxx, experimentData = experimentData)
>>
>> Error in function (classes, fdef, mtable)  :
>>   unable to find an inherited method for function
>> "annotatedDataFrameFrom", for signature "data.frame"
>
> you're not providing a featureData instance, so R is trying to infer one
> from exprs. My guess is that exprs is data.frame, but should be a matrix.
>
> In R-2.14 there is the function ExpressionSet() which might make this more
> transparent
>
>> args(ExpressionSet)
> function (assayData, phenoData = annotatedDataFrameFrom(assayData,
>    byrow = FALSE), featureData = annotatedDataFrameFrom(assayData,
>    byrow = TRUE), experimentData = new("MIAME"), annotation = character(),
>    protocolData = annotatedDataFrameFrom(assayData, byrow = FALSE),
>    ...)
> NULL
>
> Martin
>
>>
>> I have done this a gazillion times before without a hitch, and
>> suddenly I'm not able to do so anymore. If anyone knows what's going
>> on, I am all ears.
>>
>> Kind regards,
>> Bas
>>
>>> sessionInfo()
>>
>> R version 2.13.2 (2011-09-30)
>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>>
>> locale:
>> [1] C/UTF-8/C/C/C/C
>>
>> attached base packages:
>> [1] splines   tools     stats     graphics  grDevices utils     datasets
>> [8] methods   base
>>
>> other attached packages:
>> [1] LMGene_2.8.0     affy_1.30.0      survival_2.36-10 multtest_2.8.0
>> [5] Biobase_2.12.2
>>
>> loaded via a namespace (and not attached):
>> [1] MASS_7.3-14           affyio_1.20.0         preprocessCore_1.14.0
>> [4] tcltk_2.13.2
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>
> --
> Computational Biology
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
>
> Location: M1-B861
> Telephone: 206 667-2793
>